Abstract:
Objective Ligand recognition of the odorant-binding protein PxylOBP31 in Plutella xylostella was investigated to decipher the olfactory mechanism of the pest.
Methods Homology modeling and molecular docking were applied to analyze PxylOBP31, the olfactory sensing-related protein specifically expressed in the antennae of P. xylostella. The Swiss model was used to construct the 3D structure of the protein to be evaluated by Procheck, Verify3D, and ERRAT. AutoDock was employed to examine the molecular docking, calculate the binding free energy, and analyze the key residues of the protein with 39 volatiles.
Results The applied model displayed a high reliability by 98.0% of the amino acid residues appearing in the highly optimal zones on the Ramachandran conformation diagram, 76.52% of them carrying a Verify 3D score greater than 0.1, and as high as 99.07% on ERRAT. The binding free energy of PxylOBP31 with the 39 ligands ranged from −7.28 kcal·mol−1 on β-caryophyllene to −3.48 kcal·mol−1 on 1-hexanol. The key binding residues, such as Gln101, Asn108, and Phe113, formed core pockets with the ligands possibly through hydrogen bonds or hydrophobic interactions.
Conclusion The molecular information revealed by this study on the mechanism of the broad-spectrum ligand recognition of PxylOBP31 provided a basis for the development of targeted olfactory regulators with precise binding pockets in the protein of P. xylostella.
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